use pre-commit.ci (#597)

* use pre-commit.ci

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* disable codespell, enable ruff autofix

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* disable some pre-commits

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* reset

* fix comment

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,41 +1,38 @@
----
-name: Bug report
-about: Create a report to help us improve
-title: ''
-labels: ''
+______________________________________________________________________
+
+name: Bug report about: Create a report to help us improve title: '' labels: ''
 assignees: ''
 
----
+______________________________________________________________________
+
+**Describe the bug** A clear and concise description of what the bug is.
 
-**Describe the bug**
-A clear and concise description of what the bug is.
+**To Reproduce** Steps to reproduce the behavior:
 
-**To Reproduce**
-Steps to reproduce the behavior:
 1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
+1. Click on '....'
+1. Scroll down to '....'
+1. See error
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+**Expected behavior** A clear and concise description of what you expected to
+happen.
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+**Screenshots** If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
 
-**System parameters**
-Please run the following in your python kernel and copy the output below.
+- OS: \[e.g. iOS\]
+- Browser \[e.g. chrome, safari\]
+- Version \[e.g. 22\]
+
+**System parameters** Please run the following in your python kernel and copy
+the output below.
 
 ```python
 import mdsuite as mds
 mds.Report()
 ```
- **Output here**
 
-**Additional context**
-Add any other context about the problem here.
+**Output here**
+
+**Additional context** Add any other context about the problem here.

.github/ISSUE_TEMPLATE/doc_report.md

@@ -1,27 +1,22 @@
----
-name: Docs report
-about: Create a report regarding the docs for us to look at.
-title: ''
-labels: ''
-assignees: ''
+______________________________________________________________________
 
----
+name: Docs report about: Create a report regarding the docs for us to look at.
+title: '' labels: '' assignees: ''
 
-**Describe the problem**
-A clear and concise description of what the bug is.
+______________________________________________________________________
+
+**Describe the problem** A clear and concise description of what the bug is.
+
+**To Reproduce** Steps to reproduce the behavior:
 
-**To Reproduce**
-Steps to reproduce the behavior:
 1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
+1. Click on '....'
+1. Scroll down to '....'
+1. See error
 
-**Expected content**
-A clear and concise description of what you expected to see.
+**Expected content** A clear and concise description of what you expected to
+see.
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+**Screenshots** If applicable, add screenshots to help explain your problem.
 
-**Additional context**
-Add any other context about the problem here.
+**Additional context** Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,20 +1,18 @@
----
-name: Feature request
-about: Suggest an idea for this project
-title: ''
-labels: ''
-assignees: ''
+______________________________________________________________________
 
----
+name: Feature request about: Suggest an idea for this project title: '' labels:
+'' assignees: ''
 
-**What feature would you like to see added?**
-A clear and concise description of the feature you would like to see added to MDSuite
+______________________________________________________________________
 
-**Describe how this feature would improve the code**
-This can be in usability, functionality, or general aesthetic.
+**What feature would you like to see added?** A clear and concise description of
+the feature you would like to see added to MDSuite
 
-**Describe how this feature would work/possible implementations**
-A clear and concise description of what you want to happen.
+**Describe how this feature would improve the code** This can be in usability,
+functionality, or general aesthetic.
 
-**Additional context**
-Add any other context or screenshots about the feature request here.
+**Describe how this feature would work/possible implementations** A clear and
+concise description of what you want to happen.
+
+**Additional context** Add any other context or screenshots about the feature
+request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,9 +1,10 @@
 <!-- The issue that is fixed by this PR, if applicable: -->
+
 Fix #
 
 #### Summary of additions and changes
 
-* 
+-
 
 #### How to test this pull request
 

.github/workflows/pytest.yml

@@ -14,11 +14,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: 
+        python-version:
         - 3.8
         - 3.9
         - "3.10"
-        
+
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}

.gitignore

@@ -151,7 +151,7 @@ mdsuite/cython_extensions/*.c
 # APPLE
 .DS_Store
 
-# pycharm 
+# pycharm
 .idea/
 
 # build documentation

.pre-commit-config.yaml

@@ -1,19 +1,45 @@
-exclude: '.git|.tox'
-default_stages: [commit]
-fail_fast: true
-
+default_language_version:
+  python: python3
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-json
+#      - id: check-merge-conflict
+#        args: ['--assume-in-merge']
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: ['--fix=lf']
+      - id: sort-simple-yaml
+      - id: trailing-whitespace
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.3.0
     hooks:
       - id: black
-
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.10.1
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
     hooks:
       - id: isort
-
+  # - repo: https://github.com/codespell-project/codespell
+  #   rev: v2.2.4
+  #   hooks:
+  #     - id: codespell
+  #       additional_dependencies: ["tomli"]
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.238
+    # Ruff version.
+    rev: 'v0.0.267'
     hooks:
       - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.16
+    hooks:
+    - id: mdformat
+      args: ["--wrap=80"]

CI/integration_tests/calculators/test_einstein_distinct_diffusion_coefficients.py

@@ -29,6 +29,7 @@
 -----
 Currently this test only checks that these calculators actually run it does not compare
 values.
+
 """
 import os
 

CONTRIBUTING.md

@@ -1,9 +1,9 @@
 # Contributing guidelines
 
-Thank you for your interest in contributing to the MDSuite code!
-Currently, MDSuite is in the process of an API change that will greatly simplify 
-external contributions as well as the code structure.
-These updates will coincide with the first full version release of the MDSuite software.
+Thank you for your interest in contributing to the MDSuite code! Currently,
+MDSuite is in the process of an API change that will greatly simplify external
+contributions as well as the code structure. These updates will coincide with
+the first full version release of the MDSuite software.
 
-For this reason, we are currently not looking for external contributions. 
-Check back in with us soon for updated details about how you can contribute.
+For this reason, we are currently not looking for external contributions. Check
+back in with us soon for updated details about how you can contribute.

LICENSE

@@ -274,4 +274,4 @@ version(s), and exceptions or additional permissions here}."
   file in a relevant directory) where a recipient would be likely to
   look for such a notice.
 
-  You may add additional accurate notices of copyright ownership.
+  You may add additional accurate notices of copyright ownership.